Here is my method:
1. Load up a skin for the aircraft you need a damage tga for.
2. Open an existing damage tga. (I prefer stock ones, since they look quite good.)
3. Load the alpha channel as a selection from the damage tga.
4. Copy the selection, then insert it over the skin of the aircraft as a new layer.
5. Move, rotate and resize the holes as needed and delete all unnecessary parts. Since you do not have an alpha channel yet, there is no need to edit it separately.
6. Make a new layer between the skin and the edited damage graphics and make it solid black.
7. Select the damage layer, load the transparency of the layer as a selection, then save it as an alpha channel.
8. Merge all the layers, then save it as a tga with the proper name. (If you want to keep it as a damage template, then save it as a psd document before merging.)